Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000090.1 Hibiscus syriacus cultivar Beakdansim tig00000165_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 111048
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:210 original size:23 final size:23
Alignment explanation
Indices: 184--370 Score: 90
Period size: 25 Copynumber: 8.1 Consensus size: 23
174 TTGATATAAT
184 ATACATATTATATAGTTTTGAAA
1 ATACATATTATATAGTTTTGAAA
*
207 ATACATATGT-T-T--TTTAGAAA
1 ATACATAT-TATATAGTTTTGAAA
* * *
227 ATATATAATATA-ATTTTTGATATA
1 ATACATATTATATAGTTTTGA-A-A
* *
251 TATATATATATATATAGTTTTTAAA
1 -ATACATAT-TATATAGTTTTGAAA
* * *
276 TAAAAATATTATATAGTATGATTTAAA
1 -ATACATATTATATAGT-T--TTGAAA
303 A-ACATATTATATAGTTTTTG-AA
1 ATACATATTATATAG-TTTTGAAA
* *
325 A-ACATATAACATAGTTTTGAAA
1 ATACATATTATATAGTTTTGAAA
*
347 AT--AT-GTATATAGTTTTTGAAA
1 ATACATATTATATAG-TTTTGAAA
368 ATA
1 ATA
371 TTTGAAAACA
Statistics
Matches: 130, Mismatches: 16, Indels: 37
0.71 0.09 0.20
Matches are distributed among these distances:
19 1 0.01
20 19 0.15
21 17 0.13
22 23 0.18
23 12 0.09
24 10 0.08
25 29 0.22
26 7 0.05
27 12 0.09
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (23 bp):
ATACATATTATATAGTTTTGAAA
Found at i:326 original size:22 final size:22
Alignment explanation
Indices: 256--368 Score: 97
Period size: 22 Copynumber: 5.0 Consensus size: 22
246 ATATATATAT
* *
256 ATATATATATAGTTTTTAAATAAAA
1 ATAT-TATATAGTTTTT-GA-AAAC
*
281 ATATTATATAGTATGATTTAAAAAC
1 ATATTATATAGT-T--TTTGAAAAC
306 ATATTATATAGTTTTTGAAAAC
1 ATATTATATAGTTTTTGAAAAC
* *
328 ATATAACATAG-TTTTG-AAA-
1 ATATTATATAGTTTTTGAAAAC
347 ATATGTATATAGTTTTTGAAAA
1 ATAT-TATATAGTTTTTGAAAA
369 TATTTGAAAA
Statistics
Matches: 76, Mismatches: 6, Indels: 15
0.78 0.06 0.15
Matches are distributed among these distances:
19 4 0.05
20 8 0.11
21 10 0.13
22 20 0.26
24 9 0.12
25 20 0.26
26 2 0.03
27 3 0.04
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.42
Consensus pattern (22 bp):
ATATTATATAGTTTTTGAAAAC
Found at i:369 original size:21 final size:20
Alignment explanation
Indices: 278--372 Score: 84
Period size: 21 Copynumber: 4.4 Consensus size: 20
268 TTTTTAAATA
*
278 AAAATATTATATAGTATGATTTAA
1 AAAATATTATATAGT-T--TTT-G
302 AAACATATTATATAGTTTTTG
1 AAA-ATATTATATAGTTTTTG
* *
323 AAAACATATAACATAG-TTTTG
1 -AAA-ATATTATATAGTTTTTG
344 AAAATATGTATATAGTTTTTG
1 AAAATAT-TATATAGTTTTTG
365 AAAATATT
1 AAAATATT
373 TGAAAACATG
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
19 4 0.06
20 9 0.15
21 17 0.27
22 16 0.26
24 4 0.06
25 12 0.19
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.42
Consensus pattern (20 bp):
AAAATATTATATAGTTTTTG
Found at i:409 original size:23 final size:25
Alignment explanation
Indices: 383--431 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
373 TGAAAACATG
383 TTACA-TA-AGTTTTAAAAAATATA
1 TTACATTATAGTTTTAAAAAATATA
*
406 TTACATTATAGTTTTTAAAAATATA
1 TTACATTATAGTTTTAAAAAATATA
431 T
1 T
432 ATAATATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.22
24 2 0.09
25 16 0.70
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (25 bp):
TTACATTATAGTTTTAAAAAATATA
Found at i:3272 original size:21 final size:22
Alignment explanation
Indices: 3222--3272 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 22
3212 ACTTATTCAC
*
3222 ATATACCT-TAACATGTACTCAT
1 ATATA-CTATAACATATACTCAT
*
3244 GTAT-CTATAACATATAC-CAT
1 ATATACTATAACATATACTCAT
3264 ATATACTAT
1 ATATACTAT
3273 CATAAAACAC
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
20 8 0.33
21 13 0.54
22 3 0.12
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.37
Consensus pattern (22 bp):
ATATACTATAACATATACTCAT
Found at i:3464 original size:23 final size:22
Alignment explanation
Indices: 3411--3484 Score: 105
Period size: 22 Copynumber: 3.4 Consensus size: 22
3401 CACCACAGCT
3411 CATATAATTGCACCGAAGTGCC
1 CATATAATTGCACCGAAGTGCC
*
3433 CATATAATTGCACCGGAGTGCC
1 CATATAATTGCACCGAAGTGCC
* *
3455 GCATAGAATTGCACCGTAGTG-C
1 -CATATAATTGCACCGAAGTGCC
3477 CATATAAT
1 CATATAAT
3485 AATGTCCATA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
21 7 0.15
22 22 0.47
23 18 0.38
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (22 bp):
CATATAATTGCACCGAAGTGCC
Found at i:3678 original size:102 final size:103
Alignment explanation
Indices: 3494--3710 Score: 364
Period size: 102 Copynumber: 2.1 Consensus size: 103
3484 TAATGTCCAT
* * *
3494 AAGGATCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATATGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATATGTCTCACCA
3559 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* * *
3597 AAGGACC-CATATCATTCCTTAAGAATCATATACATATGCCAATGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATATGTCTCACCA
*
3661 GACTTCACTCATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
3699 AAGGACCACATA
1 AAGGACCACATA
3711 GACCCTCGAC
Statistics
Matches: 106, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
102 96 0.91
103 10 0.09
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATATGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:6708 original size:14 final size:13
Alignment explanation
Indices: 6675--6712 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
6665 CCTTAAGTGA
6675 ACATTGAAG-TATG
1 ACATT-AAGATATG
6688 ACATTAAGATATG
1 ACATTAAGATATG
6701 ATCATTAAGATA
1 A-CATTAAGATA
6713 AAAACAAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 3 0.13
13 10 0.43
14 10 0.43
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.32
Consensus pattern (13 bp):
ACATTAAGATATG
Found at i:9618 original size:23 final size:22
Alignment explanation
Indices: 9574--9639 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 22
9564 TTTCAATAAG
* * *
9574 TATGCTTGTATGACACGATTTCA
1 TATGCTT-TATGGCATGTTTTCA
*
9597 TATGCCTTTATGGCATGTTTTCT
1 TATG-CTTTATGGCATGTTTTCA
*
9620 TATGCTTTTTGGCATGTTTT
1 TATGCTTTATGGCATGTTTT
9640 TTTATTGTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
22 15 0.41
23 19 0.51
24 3 0.08
ACGTcount: A:0.17, C:0.15, G:0.18, T:0.50
Consensus pattern (22 bp):
TATGCTTTATGGCATGTTTTCA
Found at i:9640 original size:23 final size:23
Alignment explanation
Indices: 9592--9644 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
9582 TATGACACGA
*
9592 TTTCATATGCCTTTATGGCATGT
1 TTTCTTATGCCTTTATGGCATGT
*
9615 TTTCTTATG-CTTTTTGGCATGT
1 TTTCTTATGCCTTTATGGCATGT
*
9637 TTTTTTAT
1 TTTCTTAT
9645 TGTTTGGACG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 19 0.70
23 8 0.30
ACGTcount: A:0.13, C:0.13, G:0.15, T:0.58
Consensus pattern (23 bp):
TTTCTTATGCCTTTATGGCATGT
Found at i:10703 original size:14 final size:14
Alignment explanation
Indices: 10686--10718 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
10676 ATTTCTATGT
*
10686 AGGGAATTATTTGC
1 AGGGAATTATTTAC
10700 AGGGAATTATTTAC
1 AGGGAATTATTTAC
10714 AGGGA
1 AGGGA
10719 TTACTCCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.30
Consensus pattern (14 bp):
AGGGAATTATTTAC
Found at i:11807 original size:22 final size:22
Alignment explanation
Indices: 11782--11826 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
11772 TTTAATTTGA
*
11782 AACAAAACTACATTGGATTAAC
1 AACAAAACTACATTGGACTAAC
* **
11804 AACAGAACTGTATTGGACTAAC
1 AACAAAACTACATTGGACTAAC
11826 A
1 A
11827 GATATTCATC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (22 bp):
AACAAAACTACATTGGACTAAC
Found at i:12783 original size:20 final size:19
Alignment explanation
Indices: 12747--12785 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
12737 TGTCTATTAT
12747 ATTTTTTTTATTTTCTTTA
1 ATTTTTTTTATTTTCTTTA
12766 ATTTTATTTT-TTTATCTTTA
1 ATTTT-TTTTATTT-TCTTTA
12786 TAATCGATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (19 bp):
ATTTTTTTTATTTTCTTTA
Found at i:14507 original size:14 final size:14
Alignment explanation
Indices: 14488--14514 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
14478 TTTGACTTAA
14488 TAATATTTCATACT
1 TAATATTTCATACT
14502 TAATATTTCATAC
1 TAATATTTCATAC
14515 GTTGTACTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.15, G:0.00, T:0.48
Consensus pattern (14 bp):
TAATATTTCATACT
Found at i:16324 original size:31 final size:31
Alignment explanation
Indices: 16289--16366 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
16279 TTTAACATCC
16289 AAGTGACCAAAACTTAATAAAACGATAACAT
1 AAGTGACCAAAACTTAATAAAACGATAACAT
* *
16320 AAGTGACCAAAACTTAATAAAACTATAACGT
1 AAGTGACCAAAACTTAATAAAACGATAACAT
16351 AAGTGACCAAAACTTA
1 AAGTGACCAAAACTTA
16367 TTTTTTTTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.53, C:0.17, G:0.10, T:0.21
Consensus pattern (31 bp):
AAGTGACCAAAACTTAATAAAACGATAACAT
Found at i:19664 original size:19 final size:19
Alignment explanation
Indices: 19640--19676 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
19630 ATCTTCCCTG
*
19640 ATTTGGATTCTCGATTTGA
1 ATTTGGATACTCGATTTGA
*
19659 ATTTGGATACTTGATTTG
1 ATTTGGATACTCGATTTG
19677 CGTTCGTGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.08, G:0.22, T:0.49
Consensus pattern (19 bp):
ATTTGGATACTCGATTTGA
Found at i:24255 original size:7 final size:7
Alignment explanation
Indices: 24243--24273 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
24233 AAATAATCCG
24243 AATTTAA
1 AATTTAA
24250 AATTTAA
1 AATTTAA
24257 AATTTAA
1 AATTTAA
24264 AATTTAA
1 AATTTAA
24271 AAT
1 AAT
24274 ATATTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
AATTTAA
Found at i:25520 original size:47 final size:47
Alignment explanation
Indices: 25451--25547 Score: 194
Period size: 47 Copynumber: 2.1 Consensus size: 47
25441 AAACATTTGT
25451 AAATATTTTATAACCATACCTCAAACACAAAACAACTTAATAAGCAA
1 AAATATTTTATAACCATACCTCAAACACAAAACAACTTAATAAGCAA
25498 AAATATTTTATAACCATACCTCAAACACAAAACAACTTAATAAGCAA
1 AAATATTTTATAACCATACCTCAAACACAAAACAACTTAATAAGCAA
25545 AAA
1 AAA
25548 CACCAAGTAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.55, C:0.21, G:0.02, T:0.23
Consensus pattern (47 bp):
AAATATTTTATAACCATACCTCAAACACAAAACAACTTAATAAGCAA
Found at i:25581 original size:20 final size:21
Alignment explanation
Indices: 25540--25581 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
25530 CAACTTAATA
25540 AGCAAAAACACCAAGTAGCAT
1 AGCAAAAACACCAAGTAGCAT
25561 AGCAAAAACACCAAGTA-CAT
1 AGCAAAAACACCAAGTAGCAT
25581 A
1 A
25582 CACTACAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.55, C:0.24, G:0.12, T:0.10
Consensus pattern (21 bp):
AGCAAAAACACCAAGTAGCAT
Found at i:33535 original size:18 final size:16
Alignment explanation
Indices: 33512--33546 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
33502 AATTCCAAGA
33512 AAATATATTAATTTTTAT
1 AAATATA-T-ATTTTTAT
33530 AAATATATATTTTTAT
1 AAATATATATTTTTAT
33546 A
1 A
33547 TTTTTATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 1 0.06
18 7 0.41
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
AAATATATATTTTTAT
Found at i:34192 original size:13 final size:13
Alignment explanation
Indices: 34174--34198 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34164 AAATATAAAT
34174 AAAACAAAATTAC
1 AAAACAAAATTAC
34187 AAAACAAAATTA
1 AAAACAAAATTA
34199 AAATGCACGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.12, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAACAAAATTAC
Found at i:35236 original size:3 final size:3
Alignment explanation
Indices: 35230--35307 Score: 106
Period size: 3 Copynumber: 26.7 Consensus size: 3
35220 ATTTATTATT
35230 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
35276 TAA TAA TTA TAA TAA TAT TTA TAA TAA AAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
35308 TAAATAAAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
2 4 0.06
3 61 0.94
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:35834 original size:122 final size:122
Alignment explanation
Indices: 35678--35967 Score: 472
Period size: 122 Copynumber: 2.4 Consensus size: 122
35668 ATTATGAACT
* *
35678 TCTTCAGATGAGTTCTTCTCATTATGAACACTTCTGGAAATGTTGATGCTGATCTATCTCCTTCT
1 TCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATGATGATCTATCTCCTTCT
* *
35743 GTGATAGAGTCATGCAAAAGGTTGAACAAGTTCTTCTCATGATGAACTTCTTCTTCC
66 GTGATAGAGTCAAGCAAAAGGTTGAACAAATTCTTCTCATGATGAACTTCTTCTTCC
* *
35800 TCTTCAGATGAGTTATTCTCATTATGAACTCTTCTGGAAATGTTGGTGATGATCTATCTCCTTCT
1 TCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATGATGATCTATCTCCTTCT
* * *
35865 TTGATAGAGTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTC
66 GTGATAGAGTCAAGCAAAAGGTTGAACAAATTCTTCTCATGATGAACTTCTTCTTCC
* *
35922 TTTTCAGATGAGTTCTTCTCATTATGAACTTCCTCTGGAAATGTTG
1 TCTTCAGATGAGTTCTTCTCATTATGAAC-TCTTCTGGAAATGTTG
35968 GTCCATCGAG
Statistics
Matches: 155, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
122 140 0.90
123 15 0.10
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.40
Consensus pattern (122 bp):
TCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATGATGATCTATCTCCTTCT
GTGATAGAGTCAAGCAAAAGGTTGAACAAATTCTTCTCATGATGAACTTCTTCTTCC
Found at i:36048 original size:36 final size:36
Alignment explanation
Indices: 36008--36205 Score: 157
Period size: 36 Copynumber: 5.5 Consensus size: 36
35998 AGTGAAACTT
* *
36008 TCTCAAGTGAGACGAATCTTGTTTTAAGAAAAACAA
1 TCTCAAGTGAGACAAATTTTGTTTTAAGAAAAACAA
* ** ** **
36044 TCTCAAGTGAGATAAATTGTTGTTTCGAGTGAAACTG
1 TCTCAAGTGAGACAAATT-TTGTTTTAAGAAAAACAA
* *
36081 TCTCAAGAGAGCCAAATTTTGTTTTAAGAAAAACAA
1 TCTCAAGTGAGACAAATTTTGTTTTAAGAAAAACAA
* * ** * **
36117 TCTCATGTGAGATAAATTTCTGTTTCGAGTAAAACTG
1 TCTCAAGTGAGACAAATTT-TGTTTTAAGAAAAACAA
** *
36154 TCTCAA--GAGACGCAGTTTGTTTTAAGAAAAACAA
1 TCTCAAGTGAGACAAATTTTGTTTTAAGAAAAACAA
* *
36188 TCTCAATTGAGATAAATT
1 TCTCAAGTGAGACAAATT
36206 ACTATTTGAA
Statistics
Matches: 117, Mismatches: 41, Indels: 8
0.70 0.25 0.05
Matches are distributed among these distances:
34 18 0.15
35 7 0.06
36 48 0.41
37 44 0.38
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (36 bp):
TCTCAAGTGAGACAAATTTTGTTTTAAGAAAAACAA
Found at i:36078 original size:73 final size:71
Alignment explanation
Indices: 35984--36205 Score: 304
Period size: 73 Copynumber: 3.1 Consensus size: 71
35974 CGAGTGGTGG
* *
35984 AAATTTCTGTTTCTAGTGAAACTTTCTCAAGTGAGACGAATCTTGTTTTAAGAAAAACAATCTCA
1 AAATTTCTGTTTCGAGTGAAACTGTCTCAAG-GAGACGAAT-TTGTTTTAAGAAAAACAATCTCA
36049 AGTGAGAT
64 AGTGAGAT
* *
36057 AAATTGT-TGTTTCGAGTGAAACTGTCTCAAGAGAGCCAAATTTTGTTTTAAGAAAAACAATCTC
1 AAATT-TCTGTTTCGAGTGAAACTGTCTCAAG-GAGACGAA-TTTGTTTTAAGAAAAACAATCTC
*
36121 ATGTGAGAT
63 AAGTGAGAT
* *
36130 AAATTTCTGTTTCGAGTAAAACTGTCTCAA-GAGACGCAGTTTGTTTTAAGAAAAACAATCTCAA
1 AAATTTCTGTTTCGAGTGAAACTGTCTCAAGGAGACG-AATTTGTTTTAAGAAAAACAATCTCAA
*
36194 TTGAGAT
65 GTGAGAT
36201 AAATT
1 AAATT
36206 ACTATTTGAA
Statistics
Matches: 133, Mismatches: 12, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
71 39 0.29
72 2 0.02
73 90 0.68
74 2 0.02
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.33
Consensus pattern (71 bp):
AAATTTCTGTTTCGAGTGAAACTGTCTCAAGGAGACGAATTTGTTTTAAGAAAAACAATCTCAAG
TGAGAT
Found at i:36085 original size:37 final size:36
Alignment explanation
Indices: 35984--36205 Score: 142
Period size: 36 Copynumber: 6.1 Consensus size: 36
35974 CGAGTGGTGG
* * *
35984 AAATTTCTGTTTCTAGTGAAACTTTCTCAAGTGAGAC
1 AAATTT-TGTTTCAAGTAAAACTATCTCAAGTGAGAC
* * * * * *
36021 GAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGAT
1 AAATTTTGTTTCAAGTAAAACTATCTCAAGTGAGAC
* * * * *
36057 AAATTGTTGTTTCGAGTGAAACTGTCTCAAGAGAGCC
1 AAATT-TTGTTTCAAGTAAAACTATCTCAAGTGAGAC
* * * * *
36094 AAATTTTGTTTTAAGAAAAACAATCTCATGTGAGAT
1 AAATTTTGTTTCAAGTAAAACTATCTCAAGTGAGAC
* *
36130 AAATTTCTGTTTCGAGTAAAACTGTCTCAA--GAGAC
1 AAATTT-TGTTTCAAGTAAAACTATCTCAAGTGAGAC
** * * * * * *
36165 GCAGTTTGTTTTAAGAAAAACAATCTCAATTGAGAT
1 AAATTTTGTTTCAAGTAAAACTATCTCAAGTGAGAC
36201 AAATT
1 AAATT
36206 ACTATTTGAA
Statistics
Matches: 132, Mismatches: 49, Indels: 9
0.69 0.26 0.05
Matches are distributed among these distances:
34 18 0.14
35 7 0.05
36 59 0.45
37 48 0.36
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.33
Consensus pattern (36 bp):
AAATTTTGTTTCAAGTAAAACTATCTCAAGTGAGAC
Found at i:36938 original size:22 final size:22
Alignment explanation
Indices: 36910--36962 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
36900 AAGTTTTAAA
36910 CTTTGAAGAGAGAATCTATCAT
1 CTTTGAAGAGAGAATCTATCAT
*
36932 CTTTGAAAAGAGAATCTATCAT
1 CTTTGAAGAGAGAATCTATCAT
36954 CTTTGAAGA
1 CTTTGAAGA
36963 ATGTAGATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (22 bp):
CTTTGAAGAGAGAATCTATCAT
Found at i:37437 original size:54 final size:54
Alignment explanation
Indices: 37328--37438 Score: 145
Period size: 54 Copynumber: 2.1 Consensus size: 54
37318 AGAATAACTG
* * *
37328 GTTCGTAAAATATTTGACAACACATTCATCATCTCATGTGGTTTCTGCTATGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTCTGCCATGAT
* *
37382 GTTCGTAAAACATTTGACAACACATTCATTC-TTTCCTGTGGCTTCTGCCCA-GAT
1 GTTCGTAAAACATTTGACAACACATTCA-TCATCTCATGTGGCTTCTG-CCATGAT
37436 GTT
1 GTT
37439 TGCCAATGAA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
54 46 0.92
55 4 0.08
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCATCTCATGTGGCTTCTGCCATGAT
Found at i:40886 original size:21 final size:21
Alignment explanation
Indices: 40860--40899 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
40850 CAGAACCCCA
*
40860 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
40881 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
40900 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:48319 original size:77 final size:77
Alignment explanation
Indices: 48169--48320 Score: 200
Period size: 77 Copynumber: 2.0 Consensus size: 77
48159 TATTTCCTGA
* *
48169 TGATATGAGCTTTCAAAATGGCCCACATAGATCATTTCTGTCTGGAATGGGCCTTCAAAATGCCC
1 TGATATGAGCCTTCAAAATGGCCCACATAGATCATTTCTGTCTGGAATGGGCCTTCAAAATACCC
*
48234 AAATATTCAAAC
66 AAACATTCAAAC
* * *
48246 TGATGTGAGCCTTCAAAAT-GCCCTACATGGATCATTTCTGTCT-GAATTGGGCCTTTAAAATAC
1 TGATATGAGCCTTCAAAATGGCCC-ACATAGATCATTTCTGTCTGGAA-TGGGCCTTCAAAATAC
**
48309 CTTAACATTCAA
64 CCAAACATTCAA
48321 TTTTTGGTAA
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
76 7 0.11
77 58 0.89
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (77 bp):
TGATATGAGCCTTCAAAATGGCCCACATAGATCATTTCTGTCTGGAATGGGCCTTCAAAATACCC
AAACATTCAAAC
Found at i:52571 original size:6 final size:6
Alignment explanation
Indices: 52529--52570 Score: 57
Period size: 6 Copynumber: 6.7 Consensus size: 6
52519 ACAAACGTAA
*
52529 AAATGC AAAGATGC AAATGC AAATGC AAATGC AAATAC AAAT
1 AAATGC -AA-ATGC AAATGC AAATGC AAATGC AAATGC AAAT
52571 ATGTAGAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
6 25 0.76
7 4 0.12
8 4 0.12
ACGTcount: A:0.55, C:0.14, G:0.14, T:0.17
Consensus pattern (6 bp):
AAATGC
Found at i:55980 original size:15 final size:16
Alignment explanation
Indices: 55954--55994 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
55944 TTTAATATCT
55954 AAAA-ATAA-AATAAA
1 AAAATATAATAATAAA
*
55968 AACAT-TAATAATAAA
1 AAAATATAATAATAAA
55983 AAAATATAATAA
1 AAAATATAATAA
55995 ATATTATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 6 0.27
15 10 0.45
16 6 0.27
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAATATAATAATAAA
Found at i:56587 original size:20 final size:20
Alignment explanation
Indices: 56562--56599 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
56552 TGCGAATATC
* *
56562 AAGATTTGCAATGCGATTGT
1 AAGATTCGCAACGCGATTGT
56582 AAGATTCGCAACGCGATT
1 AAGATTCGCAACGCGATT
56600 TTGAAAAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.29
Consensus pattern (20 bp):
AAGATTCGCAACGCGATTGT
Found at i:57097 original size:21 final size:20
Alignment explanation
Indices: 57066--57140 Score: 71
Period size: 21 Copynumber: 3.7 Consensus size: 20
57056 CATTGCGATT
*
57066 TTGGAAAATCGCAACGTGAAC
1 TTGGAATATCGCAACG-GAAC
* *
57087 TTGGATTATCGCAAC-GAAT
1 TTGGAATATCGCAACGGAAC
*
57106 TTGGAAAATCGCAACGCGAAC
1 TTGGAATATCGCAACG-GAAC
* *
57127 TTCGACTATCGCAA
1 TTGGAATATCGCAA
57141 AGAATTTGGA
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
19 16 0.37
21 27 0.63
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (20 bp):
TTGGAATATCGCAACGGAAC
Found at i:57116 original size:19 final size:19
Alignment explanation
Indices: 57065--57121 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
57055 TCATTGCGAT
57065 TTTGGAAAATCGCAACGTGAA
1 TTTGGAAAATCGCAAC--GAA
* **
57086 CTTGGATTATCGCAACGAA
1 TTTGGAAAATCGCAACGAA
57105 TTTGGAAAATCGCAACG
1 TTTGGAAAATCGCAACG
57122 CGAACTTCGA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 17 0.57
21 13 0.43
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.25
Consensus pattern (19 bp):
TTTGGAAAATCGCAACGAA
Found at i:57120 original size:40 final size:40
Alignment explanation
Indices: 57065--57150 Score: 136
Period size: 40 Copynumber: 2.1 Consensus size: 40
57055 TCATTGCGAT
* * * *
57065 TTTGGAAAATCGCAACGTGAACTTGGATTATCGCAACGAA
1 TTTGGAAAATCGCAACGCGAACTTCGACTATCGCAAAGAA
57105 TTTGGAAAATCGCAACGCGAACTTCGACTATCGCAAAGAA
1 TTTGGAAAATCGCAACGCGAACTTCGACTATCGCAAAGAA
57145 TTTGGA
1 TTTGGA
57151 CTAACGTAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (40 bp):
TTTGGAAAATCGCAACGCGAACTTCGACTATCGCAAAGAA
Found at i:57185 original size:21 final size:21
Alignment explanation
Indices: 57168--57298 Score: 106
Period size: 21 Copynumber: 6.3 Consensus size: 21
57158 AAATTTGGAA
57168 AATCGCATTGCGATTTTGTAT
1 AATCGCATTGCGATTTTGTAT
* * * * *
57189 TATCGCGTTGTGA--TAGTCAG
1 AATCGCATTGCGATTTTGT-AT
57209 AATCGCATTGCGATTTTGTAT
1 AATCGCATTGCGATTTTGTAT
* *
57230 TATCGCGTTGCGATTTTGTAT
1 AATCGCATTGCGATTTTGTAT
* * *
57251 TATCGCGTTGCGA-TTTATAT
1 AATCGCATTGCGATTTTGTAT
* * * *
57271 ATTCGAATTGCGATTTTCTAA
1 AATCGCATTGCGATTTTGTAT
57292 AATCGCA
1 AATCGCA
57299 ACGCGAAATT
Statistics
Matches: 85, Mismatches: 21, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
19 3 0.04
20 26 0.31
21 53 0.62
22 3 0.04
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.41
Consensus pattern (21 bp):
AATCGCATTGCGATTTTGTAT
Found at i:57297 original size:62 final size:62
Alignment explanation
Indices: 57166--57298 Score: 162
Period size: 62 Copynumber: 2.1 Consensus size: 62
57156 GTAAATTTGG
* * *
57166 AAAATCGCATTGCGATTTTGTATTATCGCGTTGTGATAGTCAGAATCGCATTGCGATTTTGT
1 AAAATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGAATCGAATTGCGATTTTCT
** * * *
57228 ATTATCGCGTTGCGATTTTGTATTATCGCGTTGCGATTTA-T-ATATTCGAATTGCGATTTTCT
1 AAAATCGCATTGCGATTTTGTATTATCGCGTTGCGA--TAGTCAGAATCGAATTGCGATTTTCT
57290 AAAATCGCA
1 AAAATCGCA
57299 ACGCGAAATT
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
62 55 0.95
63 1 0.02
64 2 0.03
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (62 bp):
AAAATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGAATCGAATTGCGATTTTCT
Found at i:57634 original size:17 final size:18
Alignment explanation
Indices: 57601--57636 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
57591 AATTCCAAGA
57601 AAATATATTAATTTTTAT
1 AAATATATTAATTTTTAT
*
57619 AAATATA-TATTTTTTAT
1 AAATATATTAATTTTTAT
57636 A
1 A
57637 TTTTTATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AAATATATTAATTTTTAT
Found at i:57970 original size:26 final size:26
Alignment explanation
Indices: 57941--58003 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
57931 TTAATAGAAA
*
57941 AAAATAAATAAATATTATAATT-TAAT
1 AAAATAAATAAATA-TATAATTAAAAT
* ** *
57967 AAAATATATATTTATATGATTAAAAT
1 AAAATAAATAAATATATAATTAAAAT
57993 AAAATAAATAA
1 AAAATAAATAA
58004 TAACCAAAGT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
25 6 0.21
26 23 0.79
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (26 bp):
AAAATAAATAAATATATAATTAAAAT
Found at i:59370 original size:3 final size:3
Alignment explanation
Indices: 59364--59426 Score: 76
Period size: 3 Copynumber: 21.7 Consensus size: 3
59354 ATTTATTATT
*
59364 TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA -AA TAA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
59410 TAT TTA TAA TAA AAA TA
1 TAA TAA TAA TAA TAA TA
59427 TAAATAAAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
2 4 0.08
3 46 0.92
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:59388 original size:17 final size:17
Alignment explanation
Indices: 59364--59411 Score: 71
Period size: 17 Copynumber: 2.8 Consensus size: 17
59354 ATTTATTATT
59364 TAATAATAATAATAATAA
1 TAATAATAATAATAA-AA
59382 T-ATAATAATAATAAAA
1 TAATAATAATAATAAAA
*
59398 TAATTATAATAATA
1 TAATAATAATAATA
59412 TTTATAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 3 0.11
17 24 0.86
18 1 0.04
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TAATAATAATAATAAAA
Found at i:62175 original size:37 final size:37
Alignment explanation
Indices: 62125--62254 Score: 199
Period size: 37 Copynumber: 3.5 Consensus size: 37
62115 AATTTACCGA
62125 AAATAGAAATATATTATTTATAAATCTATATTTGATT
1 AAATAGAAATATATTATTTATAAATCTATATTTGATT
62162 AAATAGAAATATATTATTTATAAATCTATATTTGATT
1 AAATAGAAATATATTATTTATAAATCTATATTTGATT
* * **
62199 AAATATAAATATATTATTTATAAATTTATATTAAATT
1 AAATAGAAATATATTATTTATAAATCTATATTTGATT
62236 AAAATACG-AATATATTATT
1 -AAATA-GAAATATATTATT
62255 ACGAATTTAT
Statistics
Matches: 86, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
37 70 0.81
38 16 0.19
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.45
Consensus pattern (37 bp):
AAATAGAAATATATTATTTATAAATCTATATTTGATT
Found at i:62186 original size:15 final size:15
Alignment explanation
Indices: 62131--62223 Score: 51
Period size: 15 Copynumber: 5.3 Consensus size: 15
62121 CCGAAAATAG
62131 AAATATATTATTTAT
1 AAATATATTATTTAT
*
62146 AAATCTATATTTGATTAAATAG
1 AAA--TATA-TT-ATT---TAT
62168 AAATATATTATTTAT
1 AAATATATTATTTAT
62183 AAATCTATATTTGATTAAATAT
1 AAA--TATA-TT-ATT---TAT
62205 AAATATATTATTTAT
1 AAATATATTATTTAT
62220 AAAT
1 AAAT
62224 TTATATTAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 28
0.67 0.02 0.30
Matches are distributed among these distances:
15 15 0.24
17 8 0.13
18 10 0.16
19 10 0.16
20 8 0.13
22 11 0.18
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (15 bp):
AAATATATTATTTAT
Found at i:62284 original size:74 final size:74
Alignment explanation
Indices: 62125--62278 Score: 186
Period size: 74 Copynumber: 2.1 Consensus size: 74
62115 AATTTACCGA
* ** *
62125 AAATAGAAATATATTATTTATAAATCTATATTTGATTAAATAGAAATATATTATTTATAAATCTA
1 AAATATAAATATATTATTTATAAATCTATATTAAATTAAATAGAAATATATTATTTACAAATCTA
* *
62190 TATTTGATT
66 TAATCGATT
* * *
62199 AAATATAAATATATTATTTATAAATTTATATTAAATTAAAATACG-AATATATTA-TTACGAATT
1 AAATATAAATATATTATTTATAAATCTATATTAAATT-AAATA-GAAATATATTATTTACAAATC
62262 TATAATCGATT
64 TATAATCGATT
62273 GAAATA
1 -AAATA
62279 CAATATTATA
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
74 48 0.71
75 19 0.28
76 1 0.01
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (74 bp):
AAATATAAATATATTATTTATAAATCTATATTAAATTAAATAGAAATATATTATTTACAAATCTA
TAATCGATT
Found at i:62647 original size:17 final size:17
Alignment explanation
Indices: 62625--62684 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
62615 AAAATAGAAA
62625 TATATTATTTATAAATC
1 TATATTATTTATAAATC
* *
62642 TATATTTGATTAAATAGAA-A
1 TATA-TT-ATT-TATA-AATC
62662 TATATTATTTATAAATC
1 TATATTATTTATAAATC
62679 TATATT
1 TATATT
62685 TGATTAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
16 2 0.06
17 13 0.38
18 5 0.15
19 5 0.15
20 7 0.21
21 2 0.06
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.50
Consensus pattern (17 bp):
TATATTATTTATAAATC
Found at i:62666 original size:37 final size:37
Alignment explanation
Indices: 62616--62745 Score: 190
Period size: 37 Copynumber: 3.5 Consensus size: 37
62606 AATTTACCGA
62616 AAATAGAAATATATTATTTATAAATCTATATTTGATT
1 AAATAGAAATATATTATTTATAAATCTATATTTGATT
62653 AAATAGAAATATATTATTTATAAATCTATATTTGATT
1 AAATAGAAATATATTATTTATAAATCTATATTTGATT
* * * **
62690 AAATATAAATACATTATTTATAAATTTATATTCAATT
1 AAATAGAAATATATTATTTATAAATCTATATTTGATT
62727 AAAATACG-AATATATTATT
1 -AAATA-GAAATATATTATT
62746 ACGAATTTAT
Statistics
Matches: 84, Mismatches: 7, Indels: 3
0.89 0.07 0.03
Matches are distributed among these distances:
37 69 0.82
38 15 0.18
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (37 bp):
AAATAGAAATATATTATTTATAAATCTATATTTGATT
Found at i:62978 original size:491 final size:491
Alignment explanation
Indices: 62056--63533 Score: 2749
Period size: 491 Copynumber: 3.0 Consensus size: 491
62046 CAAAATAGAA
62056 AAATTGAAAGTACGGTGAACAAAATAGGAGAAAGATTAAAGTTCAATGAAGAACGGTGTAATTTA
1 AAATTGAAAGTACGGTGAACAAAATAGGAGAAAGATTAAAGTTCAATGAAGAACGGTGTAATTTA
62121 CCGAAAATAGAAATATATTATTTATAAATCTATATTTGATTAAATAGAAATATATTATTTATAAA
66 CCGAAAATAGAAATATATTATTTATAAATCTATATTTGATTAAATAGAAATATATTATTTATAAA
*
62186 TCTATATTTGATTAAATATAAATATATTATTTATAAATTTATATTAAATTAAAATACGAATATAT
131 TCTATATTTGATTAAATATAAATATATTATTTATAAATTTATATTCAATTAAAATACGAATATAT
62251 TATTACGAATTTATAATCGATTGAAATACAATATTATAGTTCTAGAAGGATTGTTTTACTTTGAG
196 TATTACGAATTTATAATCGATTGAAATACAATATTATAGTTCTAGAAGGATTGTTTTACTTTGAG
* *
62316 AACCCCCATAAATATTATGCTAACCTTATAGGTTAACACAAGTTTCACAAGTTTTCATATTTCGG
261 AACCCCCATAAATATTGTGCTAACCTTATAGGTTAACACAAGTTTCAAAAGTTTTCATATTTCGG
62381 ATTTCAAGAGTTTAAAAGAAAAACCATTTTGTCTTCCACTAGTTTTTCGGTGAACTGTGCAGTGA
326 ATTTCAAGAGTTTAAAAGAAAAACCATTTTGTCTTCCACTAGTTTTTCGGTGAACTGTGCAGTGA
* ** *
62446 CAATGTAAACTCGTACTTAATAATTGATTTTATAATGATATTTTCATATTATTATCATTAAGTTT
391 CAATGTAAACTCGTACTTTATCTTTGATTTTATAATGATATTTTCATATTATTATCATTAATTTT
62511 TTTATCGGATTAACAATTTTTTAACAATCTTAAGAC
456 TTTATCGGATTAACAATTTTTTAACAATCTTAAGAC
* * *
62547 AAATTGAAAGTACAGTGAACAAAATAGGAGAAAGATTAAAGTTCAATGAGGAACAGTGTAATTTA
1 AAATTGAAAGTACGGTGAACAAAATAGGAGAAAGATTAAAGTTCAATGAAGAACGGTGTAATTTA
62612 CCGAAAATAGAAATATATTATTTATAAATCTATATTTGATTAAATAGAAATATATTATTTATAAA
66 CCGAAAATAGAAATATATTATTTATAAATCTATATTTGATTAAATAGAAATATATTATTTATAAA
*
62677 TCTATATTTGATTAAATATAAATACATTATTTATAAATTTATATTCAATTAAAATACGAATATAT
131 TCTATATTTGATTAAATATAAATATATTATTTATAAATTTATATTCAATTAAAATACGAATATAT
*
62742 TATTACGAATTTATAATCGATTGAAATACAATATTACAGTTCTAGAAGGATTGTTTTACTTTGAG
196 TATTACGAATTTATAATCGATTGAAATACAATATTATAGTTCTAGAAGGATTGTTTTACTTTGAG
*
62807 AACCCCCATAAATATTGTGCTAACCTTATAAGTTAACACAAGTTTCAAAAGTTTTCATATTTCGG
261 AACCCCCATAAATATTGTGCTAACCTTATAGGTTAACACAAGTTTCAAAAGTTTTCATATTTCGG
*
62872 ATTTCAAGAGTTTAAAAGAAAAACCATTTTGTCTTCCACTAGTTTTCCGGTGAACTGTGCAGTGA
326 ATTTCAAGAGTTTAAAAGAAAAACCATTTTGTCTTCCACTAGTTTTTCGGTGAACTGTGCAGTGA
* *
62937 CAATGTAAACTCGTACTTTATCTTTGATTTTATAATGATATTTTAATATTATTGTCATTAATTTT
391 CAATGTAAACTCGTACTTTATCTTTGATTTTATAATGATATTTTCATATTATTATCATTAATTTT
63002 TTTATCGGATTAACAATTTTTTAACAATCTTAAGAC
456 TTTATCGGATTAACAATTTTTTAACAATCTTAAGAC
63038 AAATTGAAAGTACGGTGAACAAAATAGGAGAAAGATTAAAGTTCAATGAAGAACGGTGTAATTTA
1 AAATTGAAAGTACGGTGAACAAAATAGGAGAAAGATTAAAGTTCAATGAAGAACGGTGTAATTTA
* *
63103 CCAAAAATAGAAATATATTATTTATAAATCTATATTTGATTAAATATAAATATATTATTTATAAA
66 CCGAAAATAGAAATATATTATTTATAAATCTATATTTGATTAAATAGAAATATATTATTTATAAA
63168 TCTATATTTGATTAAATATAAATATATTATTTATAAATTTATATTCAATTAAAATACGAATATAT
131 TCTATATTTGATTAAATATAAATATATTATTTATAAATTTATATTCAATTAAAATACGAATATAT
* *
63233 TATTATGAATTTATAATCGATTAAAATACAATATTATAGTTCTAGAAGGATTGTTTTACTTTGAG
196 TATTACGAATTTATAATCGATTGAAATACAATATTATAGTTCTAGAAGGATTGTTTTACTTTGAG
63298 AACCCCCATAAATATTGTGCTAACCTTATAGGTTAACACAAGTTTCAAAAGTTTTCATATTTCGG
261 AACCCCCATAAATATTGTGCTAACCTTATAGGTTAACACAAGTTTCAAAAGTTTTCATATTTCGG
63363 ATTTCAAGAGTTTAAAAGAAAAACCATTTTGTCTTCCACTAGTTTTTCGGTGAACTGTGCAGTGA
326 ATTTCAAGAGTTTAAAAGAAAAACCATTTTGTCTTCCACTAGTTTTTCGGTGAACTGTGCAGTGA
*
63428 CAATGTAAACTTGTACTTTATCTTTGATTTTATAATGATATTTTCATATTATTATCATTAATTTT
391 CAATGTAAACTCGTACTTTATCTTTGATTTTATAATGATATTTTCATATTATTATCATTAATTTT
* *
63493 TTTATCGGATTAACAAATTTTTAACAATCTGAAGAC
456 TTTATCGGATTAACAATTTTTTAACAATCTTAAGAC
63529 AAATT
1 AAATT
63534 TATTCTTAAT
Statistics
Matches: 955, Mismatches: 32, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
491 955 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.39
Consensus pattern (491 bp):
AAATTGAAAGTACGGTGAACAAAATAGGAGAAAGATTAAAGTTCAATGAAGAACGGTGTAATTTA
CCGAAAATAGAAATATATTATTTATAAATCTATATTTGATTAAATAGAAATATATTATTTATAAA
TCTATATTTGATTAAATATAAATATATTATTTATAAATTTATATTCAATTAAAATACGAATATAT
TATTACGAATTTATAATCGATTGAAATACAATATTATAGTTCTAGAAGGATTGTTTTACTTTGAG
AACCCCCATAAATATTGTGCTAACCTTATAGGTTAACACAAGTTTCAAAAGTTTTCATATTTCGG
ATTTCAAGAGTTTAAAAGAAAAACCATTTTGTCTTCCACTAGTTTTTCGGTGAACTGTGCAGTGA
CAATGTAAACTCGTACTTTATCTTTGATTTTATAATGATATTTTCATATTATTATCATTAATTTT
TTTATCGGATTAACAATTTTTTAACAATCTTAAGAC
Found at i:63157 original size:37 final size:37
Alignment explanation
Indices: 63107--63266 Score: 200
Period size: 37 Copynumber: 4.3 Consensus size: 37
63097 AATTTACCAA
* *
63107 AAATAGAAATATATTATTTATAAATCTATATTTGATT
1 AAATATAAATATATTATTTATAAATCTATATTCGATT
*
63144 AAATATAAATATATTATTTATAAATCTATATTTGATT
1 AAATATAAATATATTATTTATAAATCTATATTCGATT
* *
63181 AAATATAAATATATTATTTATAAATTTATATTCAATT
1 AAATATAAATATATTATTTATAAATCTATATTCGATT
* * *
63218 AAA-ATACGAATATATTA-TTATGAATTTATAATCGATT
1 AAATATA--AATATATTATTTATAAATCTATATTCGATT
63255 AAA-ATACAATAT
1 AAATATA-AATAT
63267 TATAGTTCTA
Statistics
Matches: 113, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
36 8 0.07
37 96 0.85
38 9 0.08
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (37 bp):
AAATATAAATATATTATTTATAAATCTATATTCGATT
Found at i:63165 original size:15 final size:15
Alignment explanation
Indices: 63113--63205 Score: 60
Period size: 15 Copynumber: 5.3 Consensus size: 15
63103 CCAAAAATAG
63113 AAATATATTATTTAT
1 AAATATATTATTTAT
63128 AAATCTATATTTGATTAAATAT
1 AAA--TATA-TT-ATT---TAT
63150 AAATATATTATTTAT
1 AAATATATTATTTAT
63165 AAATCTATATTTGATTAAATAT
1 AAA--TATA-TT-ATT---TAT
63187 AAATATATTATTTAT
1 AAATATATTATTTAT
63202 AAAT
1 AAAT
63206 TTATATTCAA
Statistics
Matches: 64, Mismatches: 0, Indels: 28
0.70 0.00 0.30
Matches are distributed among these distances:
15 16 0.25
17 8 0.12
18 10 0.16
19 10 0.16
20 8 0.12
22 12 0.19
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.48
Consensus pattern (15 bp):
AAATATATTATTTAT
Found at i:64690 original size:30 final size:30
Alignment explanation
Indices: 64654--64725 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
64644 ATAGGAATGA
*
64654 AATCCACATTCCCATGTTTGGTTGGCCTGG
1 AATCCACATTCCCATGTTTGGTTGGCCGGG
64684 AATCCACATTCCCATGTTTGGTTGGCCGGG
1 AATCCACATTCCCATGTTTGGTTGGCCGGG
*
64714 AAT-CTCATTCCC
1 AATCCACATTCCC
64726 GATAATATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 8 0.20
30 32 0.80
ACGTcount: A:0.18, C:0.29, G:0.21, T:0.32
Consensus pattern (30 bp):
AATCCACATTCCCATGTTTGGTTGGCCGGG
Found at i:72299 original size:23 final size:21
Alignment explanation
Indices: 72247--72308 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
72237 TTTTGGTGCA
*
72247 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
72267 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
72288 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
72309 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:80586 original size:13 final size:13
Alignment explanation
Indices: 80568--80593 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
80558 GAAAAAACAA
80568 TTACTGCTATAAT
1 TTACTGCTATAAT
80581 TTACTGCTATAAT
1 TTACTGCTATAAT
80594 AATTGATCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (13 bp):
TTACTGCTATAAT
Found at i:81219 original size:3 final size:3
Alignment explanation
Indices: 81202--81253 Score: 88
Period size: 3 Copynumber: 17.3 Consensus size: 3
81192 CTCATATTTT
81202 TAA TAA TTAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
81247 TAA TAA T
1 TAA TAA T
81254 TGTGTTCACA
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.04
3 42 0.89
4 3 0.06
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:90847 original size:2 final size:2
Alignment explanation
Indices: 90840--90871 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
90830 GGGGAAAAGA
90840 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
90872 CCCGTTTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:98097 original size:21 final size:21
Alignment explanation
Indices: 98072--98112 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
98062 GGAAACTACT
*
98072 CAACCACAATAGTCTACGCCC
1 CAACCACAATAATCTACGCCC
98093 CAACCACAATAATCTACGCC
1 CAACCACAATAATCTACGCC
98113 TGGCAAAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.41, G:0.07, T:0.15
Consensus pattern (21 bp):
CAACCACAATAATCTACGCCC
Found at i:106044 original size:3 final size:3
Alignment explanation
Indices: 106036--106080 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
106026 GAAGACTTCC
106036 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
106081 CTACTCTACT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:107609 original size:19 final size:17
Alignment explanation
Indices: 107578--107612 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
107568 TACATAATTC
107578 TTTTAAAAAATTATTAT
1 TTTTAAAAAATTATTAT
107595 TTTTATAAAAGATTATTA
1 TTTTA-AAAA-ATTATTA
107613 CATTTTTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 4 0.25
19 7 0.44
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (17 bp):
TTTTAAAAAATTATTAT
Done.